Contacts of the strand formed by residues 604 - 609 (chain D) in PDB entry 1HQR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 604 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B THR* 3.8 3.1 - - - +
603D LEU* 1.3 75.5 - - - +
605D ASN* 1.3 62.6 + - - -
615D ASN* 3.2 4.2 - - - +
616D LEU 2.7 29.3 + - - -
617D ASN* 2.8 21.6 + - - +
702D PHE* 3.1 28.2 - - - -
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Residues in contact with ASN 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B THR* 2.9 45.6 + - - +
281B HIS* 3.9 8.7 + - - -
410C LYS* 3.3 25.8 - - + +
604D GLY* 1.3 75.4 - - - +
606D LEU* 1.3 60.5 + - - +
607D PHE* 3.4 21.9 - - + -
614D GLN 3.9 4.0 - - - +
615D ASN* 4.3 3.1 - - - +
616D LEU* 5.3 0.7 - - - -
701D HIS* 4.0 3.0 - - - -
702D PHE* 3.0 5.9 + - - +
703D ASP* 2.9 21.8 + - - +
704D ILE* 2.8 29.8 + - - +
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Residues in contact with LEU 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604D GLY 4.3 0.2 + - - -
605D ASN* 1.3 75.1 - - - +
607D PHE* 1.3 61.2 + - - +
608D ILE* 3.7 19.4 + - + +
612D SER 4.4 1.6 - - - +
613D GLN* 4.3 1.6 - - - -
614D GLN* 2.6 48.6 + - - +
616D LEU* 3.9 25.1 - - + -
640D LEU* 4.7 2.0 - - + -
644D TYR* 3.1 45.1 - - + +
704D ILE* 3.1 37.5 - - + +
706D LEU* 4.4 6.7 - - + -
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Residues in contact with PHE 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B HIS* 4.0 8.3 - - - -
408C PHE* 4.0 32.8 - + + -
409C PHE 4.3 0.7 - - - -
410C LYS* 3.6 25.6 - - + -
605D ASN* 3.4 29.8 - - + -
606D LEU* 1.3 74.2 - - - +
608D ILE* 1.3 61.3 + - - +
609D SER 4.1 0.3 + - - -
613D GLN* 3.8 39.9 - - + +
703D ASP* 4.0 11.0 - - + -
704D ILE 2.7 22.9 + - - +
705D TYR* 3.1 37.8 - + + -
706D LEU* 2.9 21.5 + - - +
707D GLU* 5.4 0.2 - - - +
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Residues in contact with ILE 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 5.3 2.3 - - - +
408C PHE* 6.1 1.6 - - - -
606D LEU* 3.7 14.7 + - + +
607D PHE* 1.3 75.1 - - - +
609D SER* 1.3 61.8 + - - +
610D GLY 2.6 19.2 + - - -
611D GLU* 2.9 72.7 + - + +
612D SER 5.1 2.0 + - - +
614D GLN* 5.2 4.3 - - - +
644D TYR* 4.0 28.0 - - + -
653D TYR* 4.1 16.8 - - + +
706D LEU* 3.2 27.6 - - + +
708D LYS 4.1 10.1 - - - +
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Residues in contact with SER 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 5.0 5.8 - - - -
408C PHE* 5.3 10.3 - - - -
607D PHE 4.0 1.8 + - - -
608D ILE* 1.3 66.8 - - - +
610D GLY* 1.3 57.1 + - - +
611D GLU 3.7 0.2 - - - -
706D LEU 2.6 16.0 + - - -
707D GLU* 3.6 33.5 + - - -
708D LYS* 3.5 24.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il